[REVIEW]: NEEP: null empirically estimated p-values for high-throughput molecular survival analysis

[whedon]

Submitting author: @scwest (Sean West)
Repository: https://github.com/thecodingdoc/neep/
Version: 1
Editor: @majensen
Reviewers: @SiminaB, @majensen
Archive: 10.5281/zenodo.3996816

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e665412c4fecaa72ad20a9533315efd9"><img src="https://joss.theoj.org/papers/e665412c4fecaa72ad20a9533315efd9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e665412c4fecaa72ad20a9533315efd9/status.svg)](https://joss.theoj.org/papers/e665412c4fecaa72ad20a9533315efd9)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@majensen & @SiminaB, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @majensen know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @majensen

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@scwest) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @SiminaB

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@scwest) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @wrathematics, @SiminaB, @rhagenson it looks like you're currently assigned to review this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1371/journal.pone.0140072 may be missing for title: Robust selection algorithm (RSA) for multi-omic biomarker discovery; integration with functional network analysis to identify miRNA regulated pathways in multiple cancers
- https://doi.org/10.2307/2532740 may be missing for title: Maximally selected rank statistics

INVALID DOIs

- https://doi.org/10.1371/journal.pcbi.1007469 is INVALID because of 'https://doi.org/' prefix

[whedon]

👉 Check article proof 📄 👈

[rhagenson]

@majensen, after reading the conflict of interest statement and reviewing the authors of this paper I have notable conflict of interest as the last author on this paper (Dario Ghersi) is my MS thesis advisor from three years ago -- which I did not notice prior to accepting the offer to review. If you will allow me, I still would like to read the work and offer my help to its authors in the form of opening issues/PRs for necessary fixes prior to acceptance, however I do not believe my opinion can be impartially applied toward the final decision to accept/reject this work.

[majensen]

Thanks @rhagenson - I appreciate your raising this issue. I myself would definitely find it very helpful if you are willing to assist and even comment in the review. Since we have 2 other reviewers, JOSS guidelines are met. Onward!

[rhagenson]

@majensen, thank you for your understanding. To ensure I, as a commenter, am not stalling the review process I will try to get the bulk of the work done in the next few days.

Will you run the command to remove me as a reviewer, please?

@whedon remove @rhagenson as reviewer

[majensen]

@whedon remove @rhagenson as reviewer

[whedon]

OK, @rhagenson is no longer a reviewer

[rhagenson]

@scwest, I opened an issue with all the edits I see as necessary, in addition to suggested edits that I think improve quality-of-life for either yourself as maintainer or others as users.

[scwest]

I have updated the repository with the edit suggestions from @rhagenson. The Makefile and unused variable suggestions from @wrathematics have also been added.

[majensen]

@SiminaB - how are things progressing? Let me know if I can help.

[majensen]

I've heard elsewhere from Simina; she has been delayed but will turn attention to the review soon.

[SiminaB]

Apologies for the delay! My initial review is at thecodingdoc/neep#5. I think the paper needs some additional clarifications and details. I also made some suggestions for the README file and some other aspects.

[majensen]

Thanks @SiminaB!

[majensen]

@scwest how is it coming regarding thecodingdoc/neep#5?

@wrathematics -- how is your review coming along?
thanks

[majensen]

@scwest can you provide an update on progress? Thank you.

[majensen]

I've reached out to @scwest via an alternate channel for an update.

[whedon]

OK. 10.5281/zenodo.3996816 is the archive.

[majensen]

@whedon set 1 as version

[whedon]

OK. 1 is the version.

[majensen]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1371/journal.pone.0140072 may be missing for title: Robust selection algorithm (RSA) for multi-omic biomarker discovery; integration with functional network analysis to identify miRNA regulated pathways in multiple cancers
- https://doi.org/10.2307/2532740 may be missing for title: Maximally selected rank statistics
- https://doi.org/10.1111/j.2517-6161.1995.tb02031.x may be missing for title: Controlling the false discovery rate: a practical and powerful approach to multiple testing

INVALID DOIs

- https://doi.org/10.1371/journal.pcbi.1007469 is INVALID because of 'https://doi.org/' prefix

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1675

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1675, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[majensen]

@scwest - can you look at #2044 (comment) and add those refs? Re: the invalid DOI, I believe you want to reference just the "10.1371/..." portion in the bib file, and whedon adds the prefix. Thanks!

[scwest]

I have added the updated DOIs to the paper.bib file. I then prepared a new release with the changes.

[majensen]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1371/journal.pcbi.1007469 is OK
- 10.1371/journal.pone.0140072 is OK
- 10.2307/2532740 is OK
- 10.1111/j.2517-6161.1995.tb02031.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

[majensen]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1371/journal.pcbi.1007469 is OK
- 10.1371/journal.pone.0140072 is OK
- 10.2307/2532740 is OK
- 10.1111/j.2517-6161.1995.tb02031.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#1678

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1678, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[majensen]

@openjournals/joss-eics this paper is, in fact, ready. Thanks.

[arfon]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02044 joss-papers#1682
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02044
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@SiminaB, @majensen - may thanks for your reviews here and to @majensen for editing too ✨

@scwest - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02044/status.svg)](https://doi.org/10.21105/joss.02044)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02044">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02044/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02044/status.svg
   :target: https://doi.org/10.21105/joss.02044

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[scwest]

Thanks, Mark! I appreciate all the effort and hard work that came from the reviewers, but especially you! Sean

…

On Mon, Aug 31, 2020 at 1:22 AM whedon ***@***.***> wrote: 🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets: Markdown: [](https://doi.org/10.21105/joss.02044) HTML: <a style="border-width:0" href="https://doi.org/10.21105/joss.02044"> <img src="https://joss.theoj.org/papers/10.21105/joss.02044/status.svg" alt="DOI badge" > </a> reStructuredText: .. image:: https://joss.theoj.org/papers/10.21105/joss.02044/status.svg :target: https://doi.org/10.21105/joss.02044 This is how it will look in your documentation: [image: DOI] <https://doi.org/10.21105/joss.02044> *We need your help!* Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following: - Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html - Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2044 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGAU556PCFOFWRKSCXSOADDSDM6TDANCNFSM4KMG7WVA> .

[majensen]

@scwest by all means! It a nice idea made very functional, and I'm glad we could bring it in for a landing.